P1289: COMPUTATIONAL SIMULATIONS SHED LIGHT ON THE 3D CONSEQUENCE OF SUPER-ENHANCER HIJACKING IN B CELL MALIGNANCIES
Authors: L. Russell, D. Kent, A. Mikulasova, N. Karataraki, B. Walker, B. Javierre, D. Rico, C. Brackley
Journal: HemaSphere (2022)

Background: Chromosomal translocations are important drivers of haematological malignancies whereby proto-oncogenes are activated by juxtaposition with super-enhancers. The immunoglobulin (IG) and T-cell receptor loci are enhancer-rich regions that are commonly hijacked via translocation in many subtypes of lymphoid malignancies. However, the epigenomic landscape and 3D genome structure remains poorly understood. We previously analysed the epigenomic consequence of rearrangements between the super-enhancers of the IG heavy chain locus (IGH) and proto-oncogene CCND11. By integrating BLUEPRINT epigenomic data with DNA breakpoint detection, we observed a broad H3K4me3 domain (BD) within the IGH locus of healthy B-cells that was absent in samples with IGH-CCND1 translocations. Upon chromosomal translocation, we observed the appearance of an H3K4me3-BD over CCND1 concomitant with its overexpression and an extensive increase in chromatin accessibility of this locus. In addition, we observed similar cancer-specific H3K4me3-BDs associated with super-enhancer hijacking of other common oncogenes in B-cell (MAF, MYC and FGFR3/NSD2) and T-cell malignancies (LMO2, TLX3 and TAL1)1. Aims: To understand and predict the 3D genome consequence of IGH-CCND1 translocation events using the highly predictive heteromorphic polymer model (HiP-HoP). Methods: Using methods from polymer physics, HiP-HoP uses data on DNA accessibility, chromatin states, and protein binding to generate an ensemble of simulated 3D chromosome structures. After confirming that the model gives good predictions of Hi-C data for a healthy human B-cell derived cell line, we generated predictions for two B-cell malignant cell lines (U266, Z-138) possessing IGH-CCND1 rearrangements. Results: We confirmed that the insertion of a single IGH super enhancer (Eα1) in U266 leaves the local topologically associated domain (TAD) structure intact. Simulations of the reciprocal IGH-CCND1 translocation in Z-138, suggested the TAD boundaries are preserved, creating an oncogenic fusion TAD encompassing CCND1 and all four IGH super-enhancers. Further simulations suggested that it is the downstream epigenetic changes which drive the 3D structural changes, rather than the genomic rearrangement itself. This points to a scenario where the translocated IGH super-enhancers first recruit chromatin remodelers to the region; this then drives epigenomic changes which in turn disrupts the wider 3D structure leading to dysregulation of cyclin D1. The model was able to predict how the structure of CCND1 changes in these different cell lines, could simulate different breakpoints, and could predict the impact on gene expression. Using qPCR and 3D-FISH we were able to validate the predicted high mRNA expression levels and increase in volume of the CCND1 locus. Summary/Conclusion: Taken together, our analysis suggests that H3K4me3-BDs are created by super-enhancers and supports the new concept of epigenomic translocation, where the relocation of H3K4me3-BDs accompanies the translocation of super-enhancers, altering the local 3D genome. References 1. PMID:34933939